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alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

apbs-pdb2pqr

APBS and PDB2PQR software

bfee2

binding free energy estimator 2

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

colvars

Collective variables module for molecular simulation and analysis programs

dgl

Python package built to ease deep learning on graph, on top of existing DL frameworks.

flareplot

Visualization tool for changing networks

freesolv

Experimental and calculated small molecule hydration free energies

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

machinelearning

My blogs and code for machine learning. http://cnblogs.com/pinard

md-ifp

MD trajectory analysis using protein-ligand Interaction Fingerprints

msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

msmexplorer

Data visualizations for biomolecular dynamics

oddt

Open Drug Discovery Toolkit

openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

prolif

Interaction Fingerprints for protein-ligand complexes and more

pyautofep

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

ticc

ttclust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)